high performance computing on graphics processing units: hgpu.org

BACKGROUND:Many analyses of microarray association studies involve permutation and bootstrap resampling, and cross-validation, that are ideally formulated as embarrassingly parallel computing problems. Given that these analyses are computationally intensive, scalable approaches that can take advantage of multi-core processor systems need to be developed. RESULTS:We have developed a CUDA based implementation, permGPU, that employs graphics processing […]

In this paper, we propose an acceleration of collapsed variational Bayesian (CVB) inference for latent Dirichlet allocation (LDA) by using Nvidia CUDA compatible devices. While LDA is an efficient Bayesian multi-topic document model, it requires complicated computations for parameter estimation in comparison with other simpler document models, e.g. probabilistic latent semantic indexing, etc. Therefore, we […]

PURPOSE: To accelerate the simultaneous algebraic reconstruction technique (SART) with motion compensation for speedy and quality computed tomography reconstruction by exploiting CUDA-enabled GPU. METHODS: Two core techniques are proposed to fit SART into the CUDA architecture: (1) a ray-driven projection along with hardware trilinear interpolation, and (2) a voxel-driven back-projection that can avoid redundant computation […]

In recent years, it can be observed that there is a gradual increase in the number of researchers and projects involved with the development of omnidirectional vision systems for various applications. The primary factors, which contributed towards this positive trend, are the availability of inexpensive and high resolution vision sensors, robust and fast computers and […]

We developed a GPU-based analytical method, named as SHEsisEpi, which purely focuses on risk epistasis in a genome-wide association study (GWAS) of complex traits, excluding the contamination of marginal effects caused by single-locus association. We analyzed the Wellcome Trust Case Control Consortium’s (WTCCC) GWAS data of bipolar disorder (BPD) with 500K SNPs.

The robust alignment of tilt-series collected for cryo-electron tomography in the absence of fiducial markers, is a problem that, especially for tilt-series of vitreous sections, still represents a significant challenge. Here we present a complete software package that implements a cross-correlation based procedure that tracks similar image features that are present in several micrographs and […]

We present a Hessenberg reduction (HR) algorithm for hybrid systems of homogeneous multicore with GPU accelerators that can exceed 25 ? the performance of the corresponding LAPACK algorithm running on current homogeneous multicores. This enormous acceleration is due to proper matching of algorithmic requirements to architectural strengths of the system

Due to significant multi-scale heterogeneity, understanding sub-grid structures is critical to effective continuum-based description of gas-solid flow. However, it is challenging for both physical measurements and numerical simulations. In this article, with the macro-scale pseudo-particle method (MaPPM) implemented on a GPU-based HPC system, up to 30,000 fluidized solids are simulated using the N-S equation directly. […]

The use of graphics hardware for general purpose computations allows scientists to enormously speed up their numerical codes. We presently investigate the impact of this technology on our computational fluid dynamics solver for the three-dimensional two-phase incompressible Navier-Stokes equations, which is based on the level set technique and applies Chorin

Biology is inherently parallel. Models of biological systems and bio-inspired algorithms also share this parallelism, although most are simulated on serial computers. Previous work created the systemic computer – a new model of computation designed to exploit many natural properties observed in biological systems, including parallelism. The approach has been proven through two existing implementations […]

Pallalel GPGPU computing for lattice QCD simulations has a bottleneck on the GPU to GPU data communication due to the lack of the direct data exchanging facility. In this work we investigate the performance of quark solver using the restricted additive Schwarz (RAS) preconditioner on a low cost GPU cluster. We expect that the RAS […]

Application of biomechanical modeling techniques in the area of medical image analysis and surgical simulation implies two conflicting requirements: accurate results and high solution speeds. Accurate results can be obtained only by using appropriate models and solution algorithms. In our previous papers we have presented algorithms and solution methods for performing accurate nonlinear finite element […]